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- PDB-4dor: Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, in its ... -

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Basic information

Entry
Database: PDB / ID: 4dor
TitleHuman Nuclear Receptor Liver Receptor Homologue-1, LRH-1, in its apo State Bound to a Fragment of Human SHP Box1
Components
  • Nuclear receptor subfamily 0 group B member 2
  • Nuclear receptor subfamily 5 group A member 2
KeywordsTRANSCRIPTION / nuclear receptor / ligand binding domain / phospholipids / NR5A / Diabetes / phosphatidylcholine
Function / homology
Function and homology information


Regulation of gene expression in early pancreatic precursor cells / pancreas morphogenesis / calcineurin-mediated signaling / acinar cell differentiation / tissue development / bile acid metabolic process / bile acid and bile salt transport / transcription regulator inhibitor activity / peroxisome proliferator activated receptor binding / embryo development ending in birth or egg hatching ...Regulation of gene expression in early pancreatic precursor cells / pancreas morphogenesis / calcineurin-mediated signaling / acinar cell differentiation / tissue development / bile acid metabolic process / bile acid and bile salt transport / transcription regulator inhibitor activity / peroxisome proliferator activated receptor binding / embryo development ending in birth or egg hatching / nuclear thyroid hormone receptor binding / homeostatic process / positive regulation of viral genome replication / animal organ regeneration / response to glucose / nuclear retinoid X receptor binding / Notch signaling pathway / cholesterol metabolic process / cellular response to leukemia inhibitory factor / hormone-mediated signaling pathway / cholesterol homeostasis / transcription coregulator binding / phospholipid binding / circadian regulation of gene expression / SUMOylation of intracellular receptors / negative regulation of DNA-binding transcription factor activity / positive regulation of insulin secretion / response to organic cyclic compound / Nuclear Receptor transcription pathway / circadian rhythm / RNA polymerase II transcription regulator complex / transcription corepressor activity / nuclear receptor activity / sequence-specific double-stranded DNA binding / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / Estrogen-dependent gene expression / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / negative regulation of gene expression / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding / chromatin / protein-containing complex binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nuclear receptor subfamily 0 group B member 1/2 / Nuclear hormone receptor family 5 / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors ...Nuclear receptor subfamily 0 group B member 1/2 / Nuclear hormone receptor family 5 / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-EPH / Nuclear receptor subfamily 5 group A member 2 / Nuclear receptor subfamily 0 group B member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMusille, P.M. / Ortlund, E.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Antidiabetic phospholipid-nuclear receptor complex reveals the mechanism for phospholipid-driven gene regulation.
Authors: Musille, P.M. / Pathak, M.C. / Lauer, J.L. / Hudson, W.H. / Griffin, P.R. / Ortlund, E.A.
History
DepositionFeb 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1May 16, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear receptor subfamily 5 group A member 2
B: Nuclear receptor subfamily 5 group A member 2
C: Nuclear receptor subfamily 0 group B member 2
D: Nuclear receptor subfamily 0 group B member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5295
Polymers61,8194
Non-polymers7101
Water2,972165
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-28 kcal/mol
Surface area22570 Å2
MethodPISA
2
A: Nuclear receptor subfamily 5 group A member 2
C: Nuclear receptor subfamily 0 group B member 2


Theoretical massNumber of molelcules
Total (without water)30,9102
Polymers30,9102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-12 kcal/mol
Surface area12070 Å2
MethodPISA
3
B: Nuclear receptor subfamily 5 group A member 2
D: Nuclear receptor subfamily 0 group B member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6193
Polymers30,9102
Non-polymers7101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-17 kcal/mol
Surface area12360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.522, 59.439, 74.201
Angle α, β, γ (deg.)90.000, 100.130, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nuclear receptor subfamily 5 group A member 2 / Alpha-1-fetoprotein transcription factor / B1-binding factor / hB1F / CYP7A promoter-binding factor ...Alpha-1-fetoprotein transcription factor / B1-binding factor / hB1F / CYP7A promoter-binding factor / Hepatocytic transcription factor / Liver receptor homolog 1 / LRH-1


Mass: 29459.893 Da / Num. of mol.: 2 / Fragment: UNP residues 290-541
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B1F, CPF, FTF, LRH-1, NR5A2 / Plasmid: pLIC_MBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O00482
#2: Protein/peptide Nuclear receptor subfamily 0 group B member 2 / Orphan nuclear receptor SHP / Small heterodimer partner


Mass: 1449.673 Da / Num. of mol.: 2 / Fragment: UNP residues 15-28 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15466
#3: Chemical ChemComp-EPH / L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 709.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H68NO8P / Comment: phospholipid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 9.5%-15% PEG 3350, 5% glycerol, and 50 mM Bis-Tris, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→45 Å / Num. all: 42849 / Num. obs: 42806 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Net I/σ(I): 13

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.6.0091refinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
DENZOdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→27.67 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.83 / SU B: 5.731 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.355 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2196 2149 5 %RANDOM
Rwork0.1732 ---
all0.1755 42849 --
obs0.1755 42702 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.69 Å2 / Biso mean: 24.3912 Å2 / Biso min: 9.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0 Å20.36 Å2
2---0.16 Å2-0 Å2
3---0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.9→27.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3882 0 47 165 4094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224003
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.985393
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6215473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.36325.258194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51515744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7341517
X-RAY DIFFRACTIONr_chiral_restr0.0890.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212956
X-RAY DIFFRACTIONr_rigid_bond_restr4.293311266
X-RAY DIFFRACTIONr_sphericity_free8.2935165
X-RAY DIFFRACTIONr_sphericity_bonded6.07153933
LS refinement shellResolution: 1.902→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 147 -
Rwork0.198 2749 -
all-2896 -
obs-4249 94.95 %

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